Fungus Fuels Tree GrowthPoplar is the fastest growing hardwood tree in the western United States, making it an energy feedstock of particular interest to the U.S. Department of Energy (DOE). The fungus is almost always found among and within poplar trees, and in an effort to understand its influence on the plant, a team of scientists studied what happens to the tree’s physical traits and gene expression when the fungus is present.

Better Genome Editing for BioenergyCRISPR-Cas9 is a powerful, high-throughput gene-editing tool that can help scientists engineer organisms for bioenergy applications. Cas9 needs guide RNA to lead it to the correct sequence to snip—but not all guides are effective. Researchers created a set of guide RNAs that were effective against 94 percent of the genes in a lipid-prolific yeast.

Cultivating Symbiotic Antarctic MicrobesIn the Proceedings of the National Academy of Sciences, researchers employed multiple microbiology and ‘omics techniques to experimentally determine that Nanohaloarchaeota are not free-living archaea but rather symbionts.

Methane Flux in the AmazonWetlands are the single largest global source of atmospheric methane. This project aims to integrate microbial and tree genetic characteristics to measure and understand methane emissions at the heart of the Amazon rainforest.

Insights into Functional Diversity in NeurosporaThis proposal investigates the genetic bases of fungal thermophily, biomass-degradation, and fungal-bacterial interactions in Sordariales, an order of biomass-degrading fungi frequently encountered in compost and encompassing one of the few groups of thermophilic fungi.

Improving the Cacao Genome and PhytozomeAn updated reference genome for Theobroma cacao Matina 1-6 has now been completed and released by HudsonAlpha scientists, with the help of Mars Wrigley funding. The annotated genome has been updated to a high quality modern standard and includes RNA-seq data. The improved genome is available for comparative purposes on the latest version of the JGI plant portal Phytozome (phytozome-next.JGI.doe.gov).

Mining IMG/M for CRISPR-Associated ProteinsResearchers report the discovery of miniature CRISPR-associated proteins that can target single-stranded DNA. The discovery was made possible by mining the datasets in the Integrated Microbial Genomes and Microbiomes (IMG/M) suite of tools managed by the JGI. The sequences were then biochemically characterized by a team led by Jennifer Doudna’s group at UC Berkeley.

What Happens Underground Influences Global Nutrient CyclesThrough the Facilities Integrating Collaborations for User Science (FICUS) program, the Environmental Molecular Sciences Laboratory (EMSL) and the DOE Joint Genome Institute (JGI) have selected 11 proposals for support from 53 received through a joint research call.

CSP Functional Genomics Call OngoingThe CSP Functional Genomics call is to enable users to perform state-of-the-art functional genomics research and to help them translate genomic information into biological function. Proposals submitted by January 31, 2019 will be part of the next review.

Learning to LookUsing machine learning, JGI researchers combed through more than 70,000 microbial and metagenome datasets, ultimately identifying more than 10,000 inovirus-like sequences compared to the 56 previously known inovirus genomes.

JGI Early Career Researchers in mSystems Special IssueJGI researchers are among the authors who offer perspectives on what the next five years of innovation could look like. In one article, Rex Malmstrom and Emiley Eloe-Fadrosh outline more targeted approaches to reconstruct individual microbes in an environmental sample. In a separate article, Simon Roux makes a pitch for readers to get involved in the developing field of virus ecogenomics.

Hidden Giants in Forest SoilsIn Nature Communications, giant virus genomes have been discovered for the first time in a forest soil ecosystem by JGI and University of Massachusetts-Amherst researchers. Most of the genomes were uncovered using a "mini-metagenomics" approach that reduced the complexity of the soil microbial communities sequenced and analyzed.

The Science

To better understand how beneficial organisms (symbionts) are transmitted between host generations, researchers investigated the role that bacteria living within a host (endosymbionts) have on fungal host reproduction, and the reproductive genes they regulate. The bacterial endosymbiont, Burkholderia, is recognized as a mutualist, where both species of organism benefit from association, but was predicted to have evolved from a parasitic interaction with their soil fungus host, Rhizopusmicrosporus. Researchers found that endobacteria establishing control over reproduction was a likely key to this evolutionary transition. Using this model, researchers also generated the first transcriptomic dataset of sexual reproduction in early fungi and discovered genes that are critical for this process.

The Impact

In the absence of the Burkholderia endobacteria, the Rhizopus fungus cannot act as a plant pathogen, it cannot reproduce asexually, and researchers have now discovered that endobacteria also regulate its sexual reproduction. The work sheds light on a poorly understood group of oleaginous or oil-producing fungi, and the impact this mutualistic interaction has on these potential large-scale biodiesel producing fungi.

Summary

In heritable mutualisms, hosts pass on beneficial symbionts between generations. The origin of this relationship though, is often antagonistic and the parasite first needs to secure its own transmission before working with the host. Using the mutualistic relationship between the plant pathogenic fungus Rhizopus microsporus (Rm) and Burkholderia endobacteria, a collaborative effort led by researchers at Cornell University and scientists at the Joint Genome Institute, a DOE Office of Science User Facility was conducted to understand how the antagonistic-to-mutualistic transition occurs. Rhizopus is a fungal pathogen of crops, including candidate bioenergy feedstocks sunflower, and maize, and a part of the oil-producing Mucoromycotina group, about which little is known. The Cornell team cultivated and experimented with the fungi and bacteria, while the DOE JGI team sequenced and annotated a host genome (Rm ATCC 52813) as part of the 1000 Fungal Genomes project.

As reported in the November 29, 2017 issue of Nature Communications, the team found that the fungus is highly dependent on the Burkholderia endobacteria to proliferate both sexually and asexually. This dependence is consistent with the addiction model of mutualism evolution; in this case, the endobacteria control the expression of ras2-1, a gene crucial to reproductive development, making the fungus reliant on the continued presence of the bacteria. By studying the Rm-Burkholderia symbiosis model, the team was able to reconstruct the reproductive pathways in several branches of the fungal kingdom, generating the first transcriptomic dataset of sexual reproduction in early fungi to find sex relevant genes across fungi. They also uncovered candidate genes, conserved across all Mucoromycotina, that appear to be involved in identifying pheromones that are critical for this fungal reproductive pathway.

Without the mutualistic Rm-Burkholderia relationship, Rhizopus is neither a plant pathogen nor able to reproduce with ease. So far, all endosymbionts discovered in fungi have been shown to substantially impact host lipid metabolism. As these oil-producing fungi are potential sustainable sources of alternative fuels, so understanding fungal-bacterial relationships can shed light on how these interactions influence lipid production in Mucoromycotina and their potential for industrial use.

BER Contact

Daniel Drell, Ph.D.
Program Manager
Biological Systems Sciences Division
Office of Biological and Environmental Research
Office of Science
US Department of Energydaniel.drell@science.doe.gov

PI Contacts

Funding

This research was supported by the National Science Foundation and the National Institutes of Health. The work conducted by the U.S. Department of Energy Joint Genome Institute is supported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231.